[Bioc-devel] import except on Window Machine

Hervé Pagès hpages at fredhutch.org
Mon Apr 11 23:54:24 CEST 2016 

Hi Michael,

On 04/11/2016 01:23 PM, Michael Lawrence wrote:
> Yes, you're right, sorry. I didn't realize that the generic is always
> exported from a package defining methods on the generic.

What's the rationale behind this feature? It seems to be a recurrent
source of surprise and confusion. In the last couple of years I must
have fixed dozens (maybe 100+) of NAMESPACEs that import things from
the wrong place, that is, what the maintainer of the package actually
needs and should import is the foo() generic from package A, but s/he
imports a particular method from package B instead. Sometimes that
method is not even the one that they actually need. *Unfortunately*
things work for a while but break later when the random method they
import disappears from package B.

One almost always calls the generic, not a particular method directly.
So personally I never use importMethodsFrom. Don't see the need for it.
I don't even know what it does i.e. what importing a method means
exactly. AFAIK when I call the generic, dispatch on the appropriate
method works, whether I "import" that method or not...

Getting the NAMESPACE right has always been a source of struggle
for developers. Simplifying and clarifying some of the concepts
involved would help make the process a little more straightforward.

Thanks,
H.


> That can make
> the exceptions more difficult to maintain. A better syntax for this
> case might have been:
>
> import(cranPackage, override=values)
>
> But we have to live with except= for now.
>
> Michael
>
> On Mon, Apr 11, 2016 at 12:25 PM, Zhu, Lihua (Julie)
> <Julie.Zhu at umassmed.edu> wrote:
>> Thanks Michael!
>>
>> FYI, I would get a warning message if I did not use import(IRanges,
>> except=values).
>>
>> Best,
>>
>> Julie
>>
>> On 4/11/16 2:40 PM, "Michael Lawrence" <lawrence.michael at gene.com> wrote:
>>
>>> On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum <dtenenba at fredhutch.org>
>>> wrote:
>>>> In that output you sent me, it's still using roxygen (via devtools) to
>>>> create the namespace. Try creating it manually and see if you still get
>>>> the same error.
>>>>
>>>> What does your NAMESPACE look like anyway?
>>>>
>>>> Looking at the NAMESPACE for CRISPRseek, the instances of the 'except'
>>>> syntax look like this:
>>>>
>>>> import(S4Vectors, except=c(fold, values))
>>>> import(IRanges, except=values)
>>>
>>> Unrelated note: should be no need to exclude values from IRanges. It
>>> is S4Vectors that exports the generic.
>>>
>>>>
>>>> So maybe make sure the objects to be excepted are not quoted?
>>>>
>>>> Dan
>>>>
>>>>
>>>>
>>>> ----- Original Message -----
>>>>> From: "Karim Mezhoud" <kmezhoud at gmail.com>
>>>>> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>>>>> Cc: "Lihua Zhu" <Julie.Zhu at umassmed.edu>, "Michael Lawrence"
>>>>> <lawrence.michael at gene.com>, "bioc-devel"
>>>>> <bioc-devel at r-project.org>
>>>>> Sent: Monday, April 11, 2016 10:21:42 AM
>>>>> Subject: Re: [Bioc-devel] import except on Window Machine
>>>>
>>>>> ##### ##    BUILT &   RELOAD
>>>>> ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
>>>>>
>>>>> * installing to library
>>>>> Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library¹
>>>>> ERROR: failed to lock directory
>>>>> Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library¹ for
>>>>> modifying
>>>>> Try removing
>>>>>
>>>>> Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/00LOCK-b
>>>>> ioCancer¹
>>>>>
>>>>> Exited with status 3.
>>>>>
>>>>> ######## BUILT SOURCE PACKAGE
>>>>> ==> devtools::document(roclets=c('rd', 'collate', 'namespace'))
>>>>>
>>>>> Updating bioCancer documentation
>>>>> Loading bioCancer
>>>>> Documentation completed
>>>>>
>>>>> ==> devtools::build()
>>>>>
>>>>> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
>>>>> --no-environ  \
>>>>>   --no-save --no-restore CMD build '/Volumes/DATA/radiant/bioCancer'  \
>>>>>   --no-resave-data --no-manual
>>>>>
>>>>> * checking for file Œ/Volumes/DATA/radiant/bioCancer/DESCRIPTION¹ ...
>>>>> OK
>>>>> * preparing ŒbioCancer¹:
>>>>> * checking DESCRIPTION meta-information ... OK
>>>>> * checking for LF line-endings in source and make files
>>>>> * checking for empty or unneeded directories
>>>>> * building ŒbioCancer_0.99.0.tar.gz¹
>>>>>
>>>>> [1] "/Volumes/DATA/radiant/bioCancer_0.99.0.tar.gz"
>>>>>
>>>>> Source package written to /Volumes/DATA/radiant
>>>>>
>>>>> On Mon, Apr 11, 2016 at 6:10 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
>>>>> wrote:
>>>>>
>>>>>> roxygen2 does not support the new syntax. Do you still get the same
>>>>>> error
>>>>>> if you write your NAMESPACE manually?
>>>>>>
>>>>>> ----- Original Message -----
>>>>>>> From: "Karim Mezhoud" <kmezhoud at gmail.com>
>>>>>>> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>>>>>>> Cc: "Lihua Zhu" <Julie.Zhu at umassmed.edu>, "Michael Lawrence" <
>>>>>> lawrence.michael at gene.com>, "bioc-devel"
>>>>>>> <bioc-devel at r-project.org>
>>>>>>> Sent: Monday, April 11, 2016 10:08:15 AM
>>>>>>> Subject: Re: [Bioc-devel] import except on Window Machine
>>>>>>
>>>>>>>> sessionInfo()
>>>>>>> R version 3.3.0 beta (2016-04-06 r70435)
>>>>>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>>>>>> Running under: OS X 10.11.3 (El Capitan)
>>>>>>>
>>>>>>> locale:
>>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Apr 11, 2016 at 6:07 PM, Dan Tenenbaum
>>>>>> <dtenenba at fredhutch.org>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Karim, What is the sessionInfo() in your R-3.3? It might be too
>>>>>> old to
>>>>>>>> have the new feature. It needs to be at svn rev r70426 or newer.
>>>>>>>>
>>>>>>>> Dan
>>>>>>>>
>>>>>>>>
>>>>>>>> ----- Original Message -----
>>>>>>>>> From: "Karim Mezhoud" <kmezhoud at gmail.com>
>>>>>>>>> To: "Lihua Zhu" <Julie.Zhu at umassmed.edu>
>>>>>>>>> Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Michael Lawrence"
>>>>>> <
>>>>>>>> lawrence.michael at gene.com>, "bioc-devel"
>>>>>>>>> <bioc-devel at r-project.org>
>>>>>>>>> Sent: Monday, April 11, 2016 10:03:52 AM
>>>>>>>>> Subject: Re: [Bioc-devel] import except on Window Machine
>>>>>>>>
>>>>>>>>> Dear Julie,
>>>>>>>>> Are you using roxigen2 to edit NAMESPACE file?
>>>>>>>>> Are you using R 3.4?
>>>>>>>>> Thanks
>>>>>>>>>
>>>>>>>>> In my case, When I used R 3.3 I get this error:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
>>>>>>>>>
>>>>>>>>> * installing to library
>>>>>>>>> Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library¹
>>>>>>>>> * installing *source* package ŒbioCancer¹ ...
>>>>>>>>> ** R
>>>>>>>>> ** inst
>>>>>>>>> ** preparing package for lazy loading
>>>>>>>>> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
>>>>>>>> vI[[i]])
>>>>>>>>> :
>>>>>>>>>   there is no package called Œc("dataTableOutput",
>>>>>> "renderDataTable")¹
>>>>>>>>> ERROR: lazy loading failed for package ŒbioCancer¹
>>>>>>>>> * removing
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCanc
>>>>>> er¹
>>>>>>>>> * restoring previous
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCanc
>>>>>> er¹
>>>>>>>>>
>>>>>>>>> Exited with status 1
>>>>>>>>>
>>>>>>>>> When I used R 3.4, I get :
>>>>>>>>>
>>>>>>>>> unfortunately,
>>>>>>>>>
>>>>>>>>> Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for
>>>>>> help
>>>>>>>>> Bioconductor does not yet support R version 3.4.0
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Apr 11, 2016 at 5:30 PM, Zhu, Lihua (Julie) <
>>>>>>>> Julie.Zhu at umassmed.edu>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Thanks, Dan!
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>>
>>>>>>>>>> Julie
>>>>>>>>>>
>>>>>>>>>> On 4/11/16 12:22 PM, "Dan Tenenbaum" <dtenenba at fredhutch.org>
>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> The windows machine is still running an older version of R
>>>>>> that does
>>>>>>>> not
>>>>>>>>>>> support this NAMESPACE syntax. I will update it this week.
>>>>>>>>>>> Dan
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ----- Original Message -----
>>>>>>>>>>>> From: "Lihua Zhu" <Julie.Zhu at umassmed.edu>
>>>>>>>>>>>> To: "bioc-devel" <bioc-devel at r-project.org>
>>>>>>>>>>>> Cc: "Michael Lawrence" <lawrence.michael at gene.com>
>>>>>>>>>>>> Sent: Monday, April 11, 2016 9:18:31 AM
>>>>>>>>>>>> Subject: [Bioc-devel] import except on Window Machine
>>>>>>>>>>>
>>>>>>>>>>>> Michael,
>>>>>>>>>>>>
>>>>>>>>>>>> For some reason,  adding except clause in import in the
>>>>>> NAMESPACE
>>>>>>>> file
>>>>>>>>>>>> gives
>>>>>>>>>>>> error on window server, although it runs fine on Linux and
>>>>>> Mac OS
>>>>>> X.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_ch
>>>>>> ec
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>>> kResults_devel_bioc-2DLATEST_CRISPRseek_moscato2-2Dbuildsrc.html&d=BQ
>>>>>>>> ICaQ
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>>> &c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2b
>>>>>>>> gmPH
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>>> hwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw&s=l
>>>>>>>> EJWy
>>>>>>>>>>>> zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA&e=
>>>>>>>>>>>>
>>>>>>>>>>>> Here is the line that gives error.
>>>>>>>>>>>> import(S4Vectors, except=c(fold, values))
>>>>>>>>>>>>
>>>>>>>>>>>> Did I miss something? Thank!
>>>>>>>>>>>>
>>>>>>>>>>>> Best regards,
>>>>>>>>>>>>
>>>>>>>>>>>> Julie
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>       [[alternative HTML version deleted]]
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm
>>>>>> an
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>>> _listinfo_bioc-2Ddevel&d=BQICaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4D
>>>>>>>> erPl
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>>> OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B
>>>>>>>> -0yS
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>>> t37UGJMdDhnwk0JFoVzS5Cw&s=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g
>>>>>>>> &e=
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>>>
>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm
>>>>>> an_listinfo_bioc-2Ddevel&d=BQIFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4D
>>>>>> erPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=p3WrsvoaEWYRGX
>>>>>> 1hHvBYdHyfl3qSnDlhimrlUmhWc78&s=3y16NmxUwgAm1KDxESsjtgLdg1qSZ5EWMfbHqPx
>>>>>> x7Go&e=
>>
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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